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Waterloo was originally known as Prairie Rapids Crossing. The town was established near two Meskwaki American tribal seasonal camps alongside the Cedar River. It was first settled in 1845 when George and Mary Melrose Hanna and their children arrived on the east bank of the Red Cedar River (now just called the Cedar River). They were followed by the Virden and Mullan families in 1846. Evidence of these earliest families can still be found in the street names Hanna Boulevard, Mullan Avenue and Virden Creek.

On December 8, 1845, the Iowa State Register and Waterloo Herald was the first newspaper published in Waterloo.

The name Waterloo supplanted the original name, Prairie Rapids Crossing, shortly after Charles Mullan petitioned for a post office in the town. Since the signed petition did not include the name of the proposed post office location, Mullan was charged with selecting the name when he submitted the petition. Tradition has it that as he flipped through a list of other post offices in the United States, he came upon the name Waterloo. The name struck his fancy, and on December 29, 1851, a post office was established under that name.^{[citation needed]} The town was later called the same, and Mullan served as the first postmaster from December 29, 1851 until August 11, 1854.

There were two extended periods of rapid growth over the next 115 years. From 1895 to 1915, the population increased from 8,490 to 33,097, a 290% increase. From 1925 to 1960, population increased from 36,771 to 71,755. The 1895 to 1915 period was a time of rapid growth in manufacturing, rail transportation and wholesale operations. During this period the Waterloo Gasoline Traction Engine Company moved to Waterloo and, shortly after, the Rath Packing Company moved from Dubuque. Another major employer throughout the first two-thirds of the 20th century was the Illinois Central Railroad. Among the others was the less-successful brass era automobile manufacturer, the Maytag-Mason Motor Company.

On June 7, 1934, bank robber Tommy Carroll had a shootout with the FBI when he and his wife stopped to pick up gas. Accidentally parking next to a police car and wasting time dropping his gun and picking it back up, Carroll was forced to flee into an alley, where he was shot. He was taken to Allen Memorial Hospital in Waterloo, where he soon died.

Waterloo suffered in the agricultural recession of the 1980s; its major employers at the time were heavily rooted in agriculture. John Deere, the area's largest employer, cut 10,000 jobs, and the Rath meatpacking plant closed altogether, losing 2500 jobs. It is estimated that Waterloo lost 14% of its population during this time. Today the city enjoys a broader industrial base, as city leaders have sought to diversify its industrial and commercial mix. Deere remains a strong presence in the city, but employs only roughly one-third the number of people it did at its peak.

In 1910, a significant number of black railroad workers were brought in as strikebreakers to the Waterloo area. Black workers were relegated to 20 square blocks in Waterloo, an area that remains the east side to this day. In 1940, more black strikebreakers were brought in to work in the Rath meat plant. In 1948, a black strikebreaker accidentally killed a white union member as he tried to escape the striker's ire. Instead of a race riot, a strike ensued against the Rath Company. The National Guard was called in to end the 73-day strike.

United Packinghouse Workers of America became the main union of the Rath Company, welcoming black workers, but United Auto Workers Local 838 continued to refuse black members. With the power of the union, Anna Mae Weems, Ada Treadwell, Charles Pearson and Jimmy Porter formed an anti-discrimination department at Rath by the 1950s. This department helped organize protests against local places that discriminated against blacks.

Porter would go on to organize the first black radio station in Waterloo, KBBG, in 1978. Weems became the head of the anti-discrimination department and local NAACP chapter.

On May 31, 1966, Eddie Wallace Sallis was found dead in the local jail. The black community felt the death was suspicious, and protests were held. On June 4, Weems led a march on city hall to encourage investigation into his death. The march led to the creation of the Waterloo Human Rights Commission, which lasted only a year due to lack of funding.

On Sept. 7, 1967, a city report, "Waterloo's Unfinished Business", was released. The report covered the ongoing problems in housing, education and employment faced by Waterloo's black community. It confirmed the housing bias faced by black residents, that many of the schools were generally 80% of one race, and that 80% of black residents held service jobs. In a 2007 article, the Courier covered some changes in the 40 years since, finding that housing was now mostly divided by socioeconomic status, schools still violated the desegregation plan, and black unemployment was still double that of white residents.

The Iowa Supreme Court outlawed school segregation in 1868. A 1967 commission found most schools were still segregated and recommended immediate desegregation, which Mayor Lloyd Turner opposed. In 1969, the Waterloo school board voted to allow open enrollment in all their schools to encourage integration. Many parents felt it was not enough. Despite the efforts between 1967 and 1970, already-black schools in the area increased in their segregation.

By the 1960s, Rath was in decline and jobs there were harder to come by. A federal government program trained 1,200 local youths with the promise of summer jobs, only to hire two as bricklayers. Starting in the summer months of 1966, Waterloo was subject to riots over race relations between the white community and the black community. Many white residents expressed confusion as to why riots were occurring in Waterloo, while younger black residents felt they were being treated unfairly, as their conditions seemed worse than those of their white neighbors. In 1967, the black population of Waterloo was equivalent to 8%, and according to the Courier, had a 4% unemployment rate. Yet despite being a northern city, Waterloo was unofficially segregated at the time, as 95% of its black population lived in "East" Waterloo. While the white community felt East High was "integrated" with a 45% black student body, the black community pointed out that the elementary school in "East" Waterloo had only one white pupil.

Protests were mostly organized by black youths aged 16–25. Protests became riots when the youth felt protesting wasn't effective. Protests turned into riots in July 1968 and reached critical mass by that September, with buildings on East 4th street torched and vandalized.

In August 1968, East High students Terri and Kathy Pearson gave the principal a list of grievances detailing how they felt the discrimination could be lessened. The principal refused to implement any of the requested changes. Student protests and walkouts continued through September. Students were angry that no African American history course was being taught, and that interracial dating was discouraged by teachers and administrators.

On Sep 13, 1968, during an East High School football game, police attempted to arrest a black youth. He resisted arrest, drawing attention of students in the stands. Black students fought and argued with the police, and police responded by using clubs and mace. The riot continued into the east side of Waterloo, with a subsequent fire that claimed a lumber mill and three homes. There was an attempt to set East High on fire as well. The riot lasted until midnight and resulted in seven officers injured and thirteen youths jailed. The National Guard was called in the following day. The riots were called off and a solution was reached thanks to civil rights leader William G Parker

In 2003, Governor Tom Vilsack created a task force to close the racial achievement gap in Waterloo. In 2009, a fair housing report, "Analysis of Impediments to Fair Housing Choice", compiled by Mullin & Lonergan Associates Inc., found Waterloo to be Iowa's most segregated city. "Historical patterns of racial segregation persist in Waterloo. Of the 20 cities in Iowa with populations exceeding 25,000, Waterloo ranks as the most segregated."

Many activists who participated in the original protests feel that Waterloo has remained the same. In 2015, Huffpost listed Waterloo as the 10th worst city for black Americans. The site noted that black residents of the city have a 24% unemployment rate compared to 3.9% for whites, giving Waterloo one of the highest black unemployment rates among Midwest cities. Waterloo still has a higher percentage of blacks than most Iowa cities.

In December 2012, Derrick Ambrose Jr. was shot by a police officer. Ambrose's family maintains he was unarmed, while the officer stated that he felt his life was in danger. A grand jury acquitted the officer. The shooting sparked outrage in the community.

June 2008 saw the worst flooding the Waterloo – Cedar Falls area had ever recorded; other major floods include the Great Flood of 1993. The flood control system constructed in the 1970s–90s largely functioned as designed.

In areas not protected by the system, the Cedar River poured out of its banks and into parking lots, backyards and across the farmland surrounding the city. Although much damage was done, the larger downstream city of Cedar Rapids was much harder hit.

An area of the west side of the downtown and an area near the former Rath Packing facility were impacted, not directly by water coming from the river, but as a result of storm runoff draining toward the river but then being trapped on the back side of the flood levy system. These areas did not have lift stations or alternate pumping capacity sufficient to force this water back to the river side of the control system. Areas where lift stations had been constructed (Virden Creek and East 7th Street) to pump this storm runoff into the swollen river remained largely dry (the east and north sides of downtown). Several areas experienced water seeping into basements due to high water-table levels.

According to the National Weather Service, the ten highest crests of the Cedar River recorded at East 7th Street in downtown Waterloo:

Crests reported in the 1960s and earlier were before completion of major flood control projects and therefore may not be directly comparable.

In September 2016, flood watches and warnings were put into effect for Waterloo and its surrounding cities. The crest was expected to just barely hit the height of the 2008 flood.

As of the census of 2010, there were 68,406 people, 28,607 households, 17,233 families residing in the city. The population density was 1,114.3 inhabitants per square mile (430.2/km²). There were 30,723 housing units at an average density of 500.5 per square mile (193.2/km²). The racial makeup of the city was 77.3% White, 15.5% African American, 0.3% Native American, 1.1% Asian, 0.3% Pacific Islander, 2.6% from other races, and 3.0% from two or more races. Hispanic or Latino people of any race were 5.6% of the population.

There were 28,607 households, of which 29.9% had children under the age of 18 living with them, 40.3% were married couples living together, 14.9% had a female householder with no husband present, 5.1% had a male householder with no wife present, and 39.8% were non-families. 31.6% of all households were made up of individuals, and 11.2% had someone living alone who was 65 years of age or older. The average household size was 2.35 and the average family size was 2.95.

The median age in the city was 35.9 years. 23.7% of residents were under the age of 18; 10.4% were between the ages of 18 and 24; 26.4% were from 25 to 44; 25.5% were from 45 to 64; and 14% were 65 years of age or older. The gender makeup of the city was 48.4% male and 51.6% female.

As of the 2000 census, there were 68,747 people, 28,169 households, and 17,746 families residing in the city. The population density was 1,131.9 inhabitants per square mile (437.0/km²). There were 29,499 housing units at an average density of 485.7 per square mile (187.5/km²). The racial makeup of the city was 79.2% White, 14.5% African American, 1.1% Asian, 1.9% from other races, and 2.0% from two or more races. Hispanic or Latino people of any race were 3.2% of the population.

There were 28,169 households, out of which 29.0% had children under the age of 18 living with them, 46.0% were married couples living together, 13.3% had a female householder with no husband present, and 37.0% were non-families. 30.0% of all households were made up of individuals, and 12.1% had someone living alone who was 65 years of age or older. The average household size was 2.39 and the average family size was 2.97.

Age spread: 24.7% under the age of 18, 10.6% from 18 to 24, 27.5% from 25 to 44, 22.0% from 45 to 64, and 15.3% who were 65 years of age or older. The median age was 36 years. For every 100 females, there were 92.2 males. For every 100 females age 18 and over, there were 88.0 males.

The median income for a household in the city was $34,092, and the median income for a family was $42,731. Males had a median income of $31,491 versus $22,569 for females. The per capita income for the city was $18,558. About 10.0% of families and 13.7% of the population were below the poverty line, including 18.6% of those under age 18 and 10.5% of those age 65 or over.

The Waterloo-Cedar Falls Metropolitan Statistical Area consists of Black Hawk, Bremer, and Grundy counties. The area had a 2000 census population of 163,706 and a 2008 estimated population of 164,220.

Waterloo is next to Cedar Falls, home to the University of Northern Iowa. Small suburbs include Evansdale, Hudson, Raymond, Elk Run Heights, Gilbertville, and Washburn.

The largest employers in the Waterloo/Cedar Falls MSA, according to the Greater Cedar Valley Alliance, as of June 2016 include (in order): John Deere, Tyson Fresh Meats, Wheaton Franciscan Healthcare, UnityPoint Health, the University of Northern Iowa, HyVee Food Stores, Waterloo Community Schools, Target Regional Distribution Center, CBE Companies, Inc., City of Waterloo, and Bertch Cabinet Manufacturing.